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Johnson was born Los Angeles, and raised in Oak Park/Agoura (which he moved to when he was in fifth grade), a suburban town about 30 miles north of Los Angeles. Johnson attended Oak Park High School his freshman year before transferring to Notre Dame High School in Sherman Oaks, California. He earned Parade, PrepStar, Football News and USA Today All-America first-team honors as a senior. Johnson recorded 104 tackles, including 32 for loss, and 17 sacks as a senior for the Knights while also setting school records for career sacks (61), tackles for loss (77), forced fumbles (14) and blocked punts (five).

Before attending Notre Dame High School, Johnson played for his hometown of Oak Park, CA for one year, playing JV football and Varsity basketball.

He also played forward on the basketball team, and in track and field he competed in the shot put and the 100 meter dash. Johnson, a highly touted recruit coming out of high school, chose to attend Florida State University. After underachieving for three years, he enjoyed a breakout senior season. He started all 12 games at left defensive tackle during his senior year and was an All-ACC first-team choice after recording 50 tackles with 2.5 sacks, 18 tackles for loss and 12 quarterback pressures.

Projected as a mid-first rounder by Sports Illustrated, Johnson was ranked as the No. 1 defensive tackle available in the 2005 NFL Draft.[2] Johnson was selected by the Houston Texans in the first round (16th overall). Johnson saw limited playing time due to injuries.